RetrogeneDB ID:

retro_btau_1410

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:5:19459781..19460810(-)
Located in intron of:ENSBTAG00000000687
Retrocopy
information
Ensembl ID:ENSBTAG00000033608
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSBTAG00000009037
Aliases:None
Description:polypeptide N-acetylgalactosaminyltransferase 12 [Source:RefSeq peptide;Acc:NP_001093795]


Retrocopy-Parental alignment summary:






>retro_btau_1410
TGTAAGTCCAAGAAGTTTAACTACAGGCGACTTCCGACCACTTCTGTCATCATCGCTTTCTATAACGAAGCCTGGTCGAC
TTTACTTCGCACCATCCACAGTGTTTTAGAAACTTCTCCCGCAGTCCTTCTGAAGGAGATCATCTTAGTCGATGACTTGA
GCGACAGAGTATATTTGAAGACACAGCTTGAAACTTACGTCAGCAATCTGGATCGAGTCCGCCTGATTAGAACAAACAAG
CGGGAAGGGCTGGTGAGGGCCCGTCTGATTGGGGCCACTTTTGCCACTGGCGATGTCCTCACTTTCCTGGATTGTCACTG
TGAGTGTAATACTGGTTGGCTGGAGCCACTTTTGGAAAGGATTCGTAAGGATGAAACAGTGGTCATTTGTCCTGTTATAG
ACACCATCGACTGGAATACTTTTGAATTCTATATGCAGACTGGGGAGCCCATGATTGGTGGGTTCGACTGGCGTCTGACA
TTCCAGTGGCATTCTGTTCCCAAACATGAAAGGGACAGGCGTAAATCGAGAATTGAACCATTCAGATCGCCCACCATGGC
CGGAGGACTGTTTGCAGTCAGCAAGAAGTATTTTCAGTACCTTGGAACTTACGATACTGGGATGGAAGTGTGGGGAGGTG
AAAACCTGGAGCTGTCTTTCAGGGTGTGGCAGTGTGGAGGTAAACTGGAGATCCACCCATGTTCCCACGTGGGCCACGTA
TTCCCTAAGCGGGCACCATATGCTCGGCCCAATTTCCTGCAGAATACTGCTCGGGCAGCGGAAGTCTGGATGGACGAGTA
CAAAGAGCATTTCTACAACCGAAACCCTCCAGCAAGGAAAGAAGCTTATGGCGATATTTCTGAAAGAAAATTACTACGGG
AAAGGCTGAGGTGCAAGAGCTTTGACTGGTATTTGAAAAATGTGTTTTCTACTTTGCATGTTCCAGAGGATAGGCCAGGC
TGGCACGGAGCTATTCGCAGTATTGGGATCTCTTCTGAATGTTTAGATTATAATGCTCCTGACAACAAC

ORF - retro_btau_1410 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.93 %
Parental protein coverage: 73.61 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalCKEKKYNYDELPTTSVVIAFYNEAWSTLLRTVYSVLETSPDTLLEEVILVDDYRDREHLKERLATELAGL
CK.KK.NY..LPTTSV.IAFYNEAWSTLLRT..SVLETSP..LL.E.ILVDD..DR..LK..L.T....L
RetrocopyCKSKKFNYRRLPTTSVIIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRVYLKTQLETYVSNL
ParentalPKVRLIRANKREGLVRARLLGASVAKGDVLTFLDCHCECHEGWLEPLLQRIHEKESAVVCPVIDVIDWNT
..VRLIR.NKREGLVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLL.RI...E..V.CPVID.IDWNT
RetrocopyDRVRLIRTNKREGLVRARLIGATFATGDVLTFLDCHCECNTGWLEPLLERIRKDETVVICPVIDTIDWNT
ParentalFEYLGNAGEPQIGGFDWRLVFTWHTVPEKERIRMRSPIDVIRSPTMAGGLFAVSKKYFEYLGSYDIGMEV
FE.....GEP.IGGFDWRL.F.WH.VP..ER.R..S.I...RSPTMAGGLFAVSKKYF.YLG.YD.GMEV
RetrocopyFEFYMQTGEPMIGGFDWRLTFQWHSVPKHERDRRKSRIEPFRSPTMAGGLFAVSKKYFQYLGTYDTGMEV
ParentalWGGENLEFSFRIWQCGGTLEIHPCSHVGHVFPRQAPYSRNKALANSVRAAEVWMDEFKELYYHRNPQARL
WGGENLE.SFR.WQCGG.LEIHPCSHVGHVFP..APY.R...L.N..RAAEVWMDE.KE..Y.RNP.AR.
RetrocopyWGGENLELSFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYKEHFYNRNPPARK
ParentalEPFGDVTERRQLRARLGCKDFKWFLNTVYPELHVPEDRPGFFGMLQNKGLRDYCFDYNPPNEH
E..GD..ER..LR.RL.CK.F.W.L..V...LHVPEDRPG..G.....G....C.DYN.P...
RetrocopyEAYGDISERKLLRERLRCKSFDWYLKNVFSTLHVPEDRPGWHGAIRSIGISSECLDYNAPDNN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
ERP005899_liver 0 .29 RPM 4 .33 RPM
ERP005899_muscle 16 .10 RPM 50 .26 RPM
SRP017611_brain 0 .32 RPM 1 .74 RPM
SRP017611_kidney 5 .93 RPM 22 .05 RPM
SRP017611_liver 0 .68 RPM 5 .06 RPM
SRP030211_testis 0 .27 RPM 10 .79 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_1410 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1410 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1410 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_777
Gorilla gorilla retro_ggor_890
Pongo abelii retro_pabe_949
Macaca mulatta retro_mmul_888
Mus musculus retro_mmus_183
Rattus norvegicus retro_rnor_2453
Oryctolagus cuniculus retro_ocun_1260
Equus caballus retro_ecab_52
Parental genes homology:
Parental genes homology involve 34 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000023021 retrocopy
retro_acar_54,
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
retro_amel_93,
Anas platyrhynchos ENSAPLG000000121971 retrocopy
retro_apla_8,
Bos taurus ENSBTAG00000009037 1 retrocopy
retro_btau_1410 ,
Bos taurus ENSBTAG000000112061 retrocopy
retro_btau_581,
Canis familiaris ENSCAFG000000024941 retrocopy
retro_cfam_683,
Cavia porcellus ENSCPOG000000124181 retrocopy
retro_cpor_1467,
Equus caballus ENSECAG000000165461 retrocopy
retro_ecab_52,
Ficedula albicollis ENSFALG000000051881 retrocopy
retro_falb_8,
Felis catus ENSFCAG000000088311 retrocopy
retro_fcat_126,
Gorilla gorilla ENSGGOG000000057921 retrocopy
retro_ggor_890,
Loxodonta africana ENSLAFG000000220111 retrocopy
retro_lafr_536,
Meleagris gallopavo ENSMGAG000000072441 retrocopy
retro_mgal_1,
Microcebus murinus ENSMICG000000110751 retrocopy
retro_mmur_282,
Myotis lucifugus ENSMLUG000000026301 retrocopy
retro_mluc_804,
Macaca mulatta ENSMMUG000000195611 retrocopy
retro_mmul_888,
Mustela putorius furoENSMPUG000000065021 retrocopy
retro_mputfur_569,
Mus musculus ENSMUSG000000397741 retrocopy
retro_mmus_183,
Nomascus leucogenys ENSNLEG000000170191 retrocopy
retro_nleu_940,
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
retro_ocun_1260,
Otolemur garnettii ENSOGAG000000014082 retrocopies
retro_ogar_3253, retro_ogar_717,
Ochotona princeps ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
retro_psin_1,
Pan troglodytes ENSPTRG000000211801 retrocopy
retro_ptro_777,
Pteropus vampyrus ENSPVAG000000087741 retrocopy
retro_pvam_1347,
Rattus norvegicus ENSRNOG000000080993 retrocopies
retro_rnor_1084, retro_rnor_1085, retro_rnor_2453,
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
retro_shar_44,
Sus scrofa ENSSSCG000000053791 retrocopy
retro_sscr_32,
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
retro_itri_41,
Tupaia belangeri ENSTBEG000000036271 retrocopy
retro_tbel_2065,
Tarsius syrichta ENSTSYG000000049751 retrocopy
retro_tsyr_386,
Tursiops truncatus ENSTTRG000000108481 retrocopy
retro_ttru_212,


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